his_emr_api_lab 1.0.5 → 1.1.3
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- checksums.yaml +4 -4
- data/README.md +20 -1
- data/app/jobs/lab/update_patient_orders_job.rb +33 -0
- data/app/jobs/lab/void_order_job.rb +18 -0
- data/app/models/lab/lab_order.rb +4 -0
- data/app/serializers/lab/lab_order_serializer.rb +7 -1
- data/app/services/lab/lims/api/couchdb_api.rb +3 -0
- data/app/services/lab/lims/api/rest_api.rb +405 -0
- data/app/services/lab/lims/api/ws_api.rb +121 -0
- data/app/services/lab/lims/config.rb +39 -2
- data/app/services/lab/lims/migrator.rb +12 -9
- data/app/services/lab/lims/order_dto.rb +8 -3
- data/app/services/lab/lims/order_serializer.rb +32 -8
- data/app/services/lab/lims/pull_worker.rb +295 -0
- data/app/services/lab/lims/push_worker.rb +104 -0
- data/app/services/lab/lims/utils.rb +6 -1
- data/app/services/lab/lims/worker.rb +42 -312
- data/app/services/lab/metadata.rb +1 -0
- data/app/services/lab/orders_search_service.rb +20 -0
- data/app/services/lab/orders_service.rb +34 -18
- data/lib/lab/version.rb +1 -1
- data/lib/tasks/loaders/data/reasons-for-test.csv +1 -0
- data/lib/tasks/loaders/data/tests.csv +0 -2
- metadata +22 -3
- data/app/services/lab/lims/failed_imports.rb +0 -33
@@ -0,0 +1,104 @@
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# frozen_string_literal: true
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module Lab
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module Lims
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class PushWorker
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attr_reader :lims_api
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include Utils # for logger
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SECONDS_TO_WAIT_FOR_ORDERS = 30
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def initialize(lims_api)
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@lims_api = lims_api
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end
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def push_orders(batch_size: 1000, wait: false)
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loop do
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logger.info('Looking for new orders to push to LIMS...')
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orders = orders_pending_sync(batch_size).all
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orders.each { |order| push_order(order) }
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# Doing this after .each above to stop ActiveRecord from executing
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# an extra request to the database (ActiveRecord's lazy evaluation
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# sometimes leads to unnecessary database hits for checking counts).
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if orders.empty? && !wait
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logger.info('Finished processing orders; exiting...')
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break
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end
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sleep(Lab::Lims::Config.updates_poll_frequency)
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end
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end
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def push_order_by_id(order_id)
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order = Lab::LabOrder.unscoped.find(order_id)
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push_order(order)
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end
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##
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# Pushes given order to LIMS queue
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def push_order(order)
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logger.info("Pushing order ##{order.order_id}")
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order_dto = Lab::Lims::OrderSerializer.serialize_order(order)
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mapping = Lab::LimsOrderMapping.find_by(order_id: order.order_id)
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ActiveRecord::Base.transaction do
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if mapping && !order.voided.zero?
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Rails.logger.info("Deleting order ##{order_dto['accession_number']} from LIMS")
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lims_api.delete_order(mapping.lims_id, order_dto)
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mapping.destroy
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elsif mapping
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Rails.logger.info("Updating order ##{order_dto['accession_number']} in LIMS")
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lims_api.update_order(mapping.lims_id, order_dto)
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mapping.update(pushed_at: Time.now)
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else
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Rails.logger.info("Creating order ##{order_dto['accession_number']} in LIMS")
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update = lims_api.create_order(order_dto)
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Lab::LimsOrderMapping.create!(order: order, lims_id: update['id'], revision: update['rev'],
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pushed_at: Time.now)
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end
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end
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order_dto
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end
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private
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def orders_pending_sync(batch_size)
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return new_orders.limit(batch_size) if new_orders.exists?
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return voided_orders.limit(batch_size) if voided_orders.exists?
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updated_orders.limit(batch_size)
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end
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def new_orders
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Rails.logger.debug('Looking for new orders that need to be created in LIMS...')
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Lab::LabOrder.where.not(order_id: Lab::LimsOrderMapping.all.select(:order_id))
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end
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def updated_orders
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Rails.logger.debug('Looking for recently updated orders that need to be pushed to LIMS...')
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last_updated = Lab::LimsOrderMapping.select('MAX(updated_at) AS last_updated')
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.first
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.last_updated
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Lab::LabOrder.left_joins(:results)
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.where('orders.discontinued_date > :last_updated
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OR obs.date_created > :last_updated',
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last_updated: last_updated)
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.group('orders.order_id')
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end
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def voided_orders
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Rails.logger.debug('Looking for voided orders that are being tracked by LIMS...')
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Lab::LabOrder.unscoped
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.where(order_type: OrderType.where(name: Lab::Metadata::ORDER_TYPE_NAME),
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order_id: Lab::LimsOrderMapping.all.select(:order_id),
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voided: 1)
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end
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end
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end
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end
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##
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# Various helper methods for modules in the Lims namespaces...
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module Utils
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LIMS_LOG_PATH = Rails.root.join('log', 'lims')
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FileUtils.mkdir_p(LIMS_LOG_PATH) unless File.exist?(LIMS_LOG_PATH)
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def logger
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Rails.logger
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end
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@@ -54,7 +57,9 @@ module Lab
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def self.parse_date(str_date, fallback_date = nil)
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str_date = str_date&.to_s
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if str_date.blank? && fallback_date.blank?
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raise "Can't parse blank date"
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end
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return parse_date(fallback_date) if str_date.blank?
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@@ -1,352 +1,82 @@
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# frozen_string_literal: true
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require '
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require 'logger_multiplexor'
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require_relative './api/couchdb_api'
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require_relative './exceptions'
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require_relative './order_serializer'
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require_relative './utils'
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module Lab
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module Lims
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LIMS_LOG_PATH = Rails.root.join('log/lims')
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Dir.mkdir(LIMS_LOG_PATH) unless File.exist?(LIMS_LOG_PATH)
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##
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# Pull/Push orders from/to the LIMS queue (Oops meant CouchDB).
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include Utils
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attr_reader :lims_api
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module Worker
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def self.start
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fout.flock(File::LOCK_EX)
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User.current = Utils.lab_user
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User.current = Utils.lab_user
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# TODO: Verify that names being pushed to LIMS are of the correct format (ie matching
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# LIMS naming conventions). Enable pushing when that is done
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worker.push_orders
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end
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end
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fork(&method(:start_push_worker))
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fork(&method(:start_pull_worker))
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fork(&method(:start_realtime_pull_worker)) if realtime_updates_enabled?
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@lims_api = lims_api
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Process.waitall
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end
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def
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orders = LabOrder.where.not(order_id: LimsOrderMapping.all.select(:order_id))
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.limit(batch_size)
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def self.start_push_worker
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start_worker('push_worker') do
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worker = PushWorker.new(lims_api)
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logger.info('No new orders available; exiting...')
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break
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end
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orders.each { |order| push_order(order) }
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worker.push_orders # (wait: true)
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end
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end
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def
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end
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##
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# Pushes given order to LIMS queue
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def push_order(order)
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logger.info("Pushing order ##{order.order_id}")
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order_dto = OrderSerializer.serialize_order(order)
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mapping = LimsOrderMapping.find_by(order_id: order.order_id)
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def self.start_pull_worker
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start_worker('pull_worker') do
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worker = PullWorker.new(lims_api)
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if mapping
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lims_api.update_order(mapping.lims_id, order_dto)
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mapping.update(pushed_at: Time.now)
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else
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update = lims_api.create_order(order_dto)
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LimsOrderMapping.create!(order: order, lims_id: update['id'], revision: update['rev'], pushed_at: Time.now)
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end
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end
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order_dto
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end
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##
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# Pulls orders from the LIMS queue and writes them to the local database
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def pull_orders(batch_size: 10_000)
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logger.info("Retrieving LIMS orders starting from #{last_seq}")
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lims_api.consume_orders(from: last_seq, limit: batch_size) do |order_dto, context|
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logger.debug("Retrieved order ##{order_dto[:tracking_number]}: #{order_dto}")
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patient = find_patient_by_nhid(order_dto[:patient][:id])
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unless patient
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logger.debug("Discarding order: Non local patient ##{order_dto[:patient][:id]} on order ##{order_dto[:tracking_number]}")
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order_rejected(order_dto, "Patient NPID, '#{order_dto[:patient][:id]}', didn't match any local NPIDs")
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next
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end
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if order_dto[:tests].empty?
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logger.debug("Discarding order: Missing tests on order ##{order_dto[:tracking_number]}")
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order_rejected(order_dto, 'Order is missing tests')
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next
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end
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diff = match_patient_demographics(patient, order_dto['patient'])
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if diff.empty?
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save_order(patient, order_dto)
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order_saved(order_dto)
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else
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save_failed_import(order_dto, 'Demographics not matching', diff)
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end
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update_last_seq(context.current_seq)
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rescue DuplicateNHID
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logger.warn("Failed to import order due to duplicate patient NHID: #{order_dto[:patient][:id]}")
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save_failed_import(order_dto, "Duplicate local patient NHID: #{order_dto[:patient][:id]}")
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rescue MissingAccessionNumber
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logger.warn("Failed to import order due to missing accession number: #{order_dto[:_id]}")
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save_failed_import(order_dto, 'Order missing tracking number')
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rescue LimsException => e
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logger.warn("Failed to import order due to #{e.class} - #{e.message}")
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save_failed_import(order_dto, e.message)
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end
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end
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protected
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def last_seq
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File.open(last_seq_path, File::RDONLY | File::CREAT, 0o644) do |fin|
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data = fin.read&.strip
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return nil if data.blank?
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return data
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end
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end
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def update_last_seq(last_seq)
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File.open(last_seq_path, File::WRONLY | File::CREAT, 0o644) do |fout|
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fout.flock(File::LOCK_EX)
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fout.write(last_seq.to_s)
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end
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end
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def order_saved(order_dto); end
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-
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def order_rejected(order_dto, message); end
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private
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def find_patient_by_nhid(nhid)
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national_id_type = PatientIdentifierType.where(name: ['National id', 'Old Identification Number'])
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identifiers = PatientIdentifier.where(type: national_id_type, identifier: nhid)
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.joins('INNER JOIN person ON person.person_id = patient_identifier.patient_id AND person.voided = 0')
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if identifiers.count.zero?
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identifiers = PatientIdentifier.unscoped
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.where(voided: 1, type: national_id_type, identifier: nhid)
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.joins('INNER JOIN person ON person.person_id = patient_identifier.patient_id AND person.voided = 0')
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worker.pull_orders
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end
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-
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# Joining to person above to ensure that the person is not voided,
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# it was noted at one site that there were some people that were voided
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# upon merging but the patient and patient_identifier was not voided
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-
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return nil if identifiers.count.zero?
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-
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patients = Patient.where(patient_id: identifiers.select(:patient_id))
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.distinct(:patient_id)
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.all
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-
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raise DuplicateNHID, "Duplicate National Health ID: #{nhid}" if patients.size > 1
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patients.first
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end
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diff = {}
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person = Person.find(local_patient.id)
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person_name = PersonName.find_by_person_id(local_patient.id)
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-
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unless (person.gender.blank? && lims_patient['gender'].blank?)\
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|| person.gender&.first&.casecmp?(lims_patient['gender']&.first)
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diff[:gender] = { local: person.gender, lims: lims_patient['gender'] }
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end
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def self.start_realtime_pull_worker
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start_worker('realtime_pull_worker') do
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worker = PullWorker.new(Lims::Api::WsApi.new(Lab::Lims::Config.updates_socket))
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41
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186
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-
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diff[:given_name] = { local: person_name&.given_name, lims: lims_patient['first_name'] }
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end
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189
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-
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190
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unless names_match?(person_name&.family_name, lims_patient['last_name'])
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diff[:family_name] = { local: person_name&.family_name, lims: lims_patient['last_name'] }
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worker.pull_orders
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end
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-
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diff
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end
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-
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197
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def names_match?(name1, name2)
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name1 = name1&.gsub(/'/, '')&.strip
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-
name2 = name2&.gsub(/'/, '')&.strip
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200
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-
|
201
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return true if name1.blank? && name2.blank?
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-
|
203
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return false if name1.blank? || name2.blank?
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-
|
205
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name1.casecmp?(name2)
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44
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end
|
207
45
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208
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def
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-
|
46
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+
def self.start_worker(worker_name)
|
47
|
+
Rails.logger = LoggerMultiplexor.new(log_path("#{worker_name}.log"), $stdout)
|
48
|
+
ActiveRecord::Base.logger = Rails.logger
|
49
|
+
Rails.logger.level = :debug
|
210
50
|
|
211
|
-
|
212
|
-
|
213
|
-
|
214
|
-
|
215
|
-
if mapping
|
216
|
-
order = update_order(patient, mapping.order_id, order_dto)
|
217
|
-
mapping.update(pulled_at: Time.now)
|
218
|
-
else
|
219
|
-
order = create_order(patient, order_dto)
|
220
|
-
mapping = LimsOrderMapping.create(lims_id: order_dto[:_id],
|
221
|
-
order_id: order['id'],
|
222
|
-
pulled_at: Time.now,
|
223
|
-
revision: order_dto['_rev'])
|
51
|
+
File.open(log_path("#{worker_name}.lock"), File::RDWR | File::CREAT, 0o644) do |fout|
|
52
|
+
unless fout.flock(File::LOCK_EX | File::LOCK_NB)
|
53
|
+
Rails.logger.warn("Another process already holds lock #{worker_name} (#{fout.read}), exiting...")
|
54
|
+
break
|
224
55
|
end
|
225
56
|
|
226
|
-
|
57
|
+
fout.write("Locked by process ##{Process.pid} under process group ##{Process.ppid} at #{Time.now}")
|
58
|
+
fout.flush
|
59
|
+
yield
|
227
60
|
end
|
228
61
|
end
|
229
62
|
|
230
|
-
def
|
231
|
-
|
232
|
-
order = OrdersService.order_test(order_dto.to_order_service_params(patient_id: patient.patient_id))
|
233
|
-
update_results(order, order_dto['test_results']) unless order_dto['test_results'].empty?
|
234
|
-
|
235
|
-
order
|
236
|
-
end
|
237
|
-
|
238
|
-
def update_order(patient, order_id, order_dto)
|
239
|
-
logger.debug("Updating order ##{order_dto['_id']}")
|
240
|
-
order = OrdersService.update_order(order_id, order_dto.to_order_service_params(patient_id: patient.patient_id)
|
241
|
-
.merge(force_update: true))
|
242
|
-
update_results(order, order_dto['test_results']) unless order_dto['test_results'].empty?
|
243
|
-
|
244
|
-
order
|
245
|
-
end
|
246
|
-
|
247
|
-
def update_results(order, lims_results)
|
248
|
-
logger.debug("Updating results for order ##{order[:accession_number]}: #{lims_results}")
|
249
|
-
|
250
|
-
lims_results.each do |test_name, test_results|
|
251
|
-
test = find_test(order['id'], test_name)
|
252
|
-
unless test
|
253
|
-
logger.warn("Couldn't find test, #{test_name}, in order ##{order[:id]}")
|
254
|
-
next
|
255
|
-
end
|
256
|
-
|
257
|
-
next unless test_results['results']
|
258
|
-
|
259
|
-
measures = test_results['results'].map do |indicator, value|
|
260
|
-
measure = find_measure(order, indicator, value)
|
261
|
-
next nil unless measure
|
262
|
-
|
263
|
-
measure
|
264
|
-
end
|
265
|
-
|
266
|
-
measures = measures.compact
|
267
|
-
next if measures.empty?
|
268
|
-
|
269
|
-
creator = format_result_entered_by(test_results['result_entered_by'])
|
270
|
-
|
271
|
-
ResultsService.create_results(test.id, provider_id: User.current.person_id,
|
272
|
-
date: Utils.parse_date(test_results['date_result_entered'], order[:order_date].to_s),
|
273
|
-
comments: "LIMS import: Entered by: #{creator}",
|
274
|
-
measures: measures)
|
275
|
-
end
|
63
|
+
def self.log_path(filename)
|
64
|
+
Lab::Lims::Utils::LIMS_LOG_PATH.join(filename)
|
276
65
|
end
|
277
66
|
|
278
|
-
def
|
279
|
-
|
280
|
-
|
281
|
-
|
282
|
-
|
283
|
-
LabTest.find_by(order_id: order_id, value_coded: test_concept.concept_id)
|
67
|
+
def self.realtime_updates_enabled?
|
68
|
+
Lims::Config.updates_socket.key?('url')
|
69
|
+
rescue Lab::Lims::Config::ConfigNotFound => e
|
70
|
+
Rails.logger.warn("Check for realtime updates failed: #{e.message}")
|
71
|
+
false
|
284
72
|
end
|
285
73
|
|
286
|
-
def
|
287
|
-
|
288
|
-
|
289
|
-
|
290
|
-
|
74
|
+
def self.lims_api
|
75
|
+
case Lims::Config.preferred_api
|
76
|
+
when /couchdb/i then Api::CouchDbApi.new(config: Lab::Lims::Config.couchdb)
|
77
|
+
when /rest/i then Api::RestApi.new(Lab::Lims::Config.rest_api)
|
78
|
+
else raise "Invalid LIMS API in application.yml, expected 'rest' or 'couchdb'"
|
291
79
|
end
|
292
|
-
|
293
|
-
value_modifier, value, value_type = parse_lims_result_value(value)
|
294
|
-
return nil if value.blank?
|
295
|
-
|
296
|
-
ActiveSupport::HashWithIndifferentAccess.new(
|
297
|
-
indicator: { concept_id: indicator.concept_id },
|
298
|
-
value_type: value_type,
|
299
|
-
value: value_type == 'numeric' ? value.to_f : value,
|
300
|
-
value_modifier: value_modifier.blank? ? '=' : value_modifier
|
301
|
-
)
|
302
|
-
end
|
303
|
-
|
304
|
-
def parse_lims_result_value(value)
|
305
|
-
value = value['result_value']&.strip
|
306
|
-
return nil, nil, nil if value.blank?
|
307
|
-
|
308
|
-
match = value&.match(/^(>|=|<|<=|>=)(.*)$/)
|
309
|
-
return nil, value, guess_result_datatype(value) unless match
|
310
|
-
|
311
|
-
[match[1], match[2], guess_result_datatype(match[2])]
|
312
|
-
end
|
313
|
-
|
314
|
-
def guess_result_datatype(result)
|
315
|
-
return 'numeric' if result.strip.match?(/^[+-]?((\d+(\.\d+)?)|\.\d+)$/)
|
316
|
-
|
317
|
-
'text'
|
318
|
-
end
|
319
|
-
|
320
|
-
def format_result_entered_by(result_entered_by)
|
321
|
-
first_name = result_entered_by['first_name']
|
322
|
-
last_name = result_entered_by['last_name']
|
323
|
-
phone_number = result_entered_by['phone_number']
|
324
|
-
id = result_entered_by['id'] # Looks like a user_id of some sort
|
325
|
-
|
326
|
-
"#{id}:#{first_name} #{last_name}:#{phone_number}"
|
327
|
-
end
|
328
|
-
|
329
|
-
def save_failed_import(order_dto, reason, diff = nil)
|
330
|
-
logger.info("Failed to import LIMS order ##{order_dto[:tracking_number]} due to '#{reason}'")
|
331
|
-
LimsFailedImport.create!(lims_id: order_dto[:_id],
|
332
|
-
tracking_number: order_dto[:tracking_number],
|
333
|
-
patient_nhid: order_dto[:patient][:id],
|
334
|
-
reason: reason,
|
335
|
-
diff: diff&.to_json)
|
336
|
-
end
|
337
|
-
|
338
|
-
def last_seq_path
|
339
|
-
LIMS_LOG_PATH.join('last_seq.dat')
|
340
|
-
end
|
341
|
-
|
342
|
-
def find_order_mapping_by_lims_id(lims_id)
|
343
|
-
mapping = Lab::LimsOrderMapping.find_by(lims_id: lims_id)
|
344
|
-
return nil unless mapping
|
345
|
-
|
346
|
-
return mapping if Lab::LabOrder.where(order_id: mapping.order_id).exists?
|
347
|
-
|
348
|
-
mapping.destroy
|
349
|
-
nil
|
350
80
|
end
|
351
81
|
end
|
352
82
|
end
|